}
}
catch(exception& e) {
- errorOut(e, "SharedUtil", "getSharedVectors");
+ m->errorOut(e, "SharedUtil", "getSharedVectors");
exit(1);
}
}
}
catch(exception& e) {
- errorOut(e, "SharedUtil", "getSharedVectorswithReplacement");
+ m->errorOut(e, "SharedUtil", "getSharedVectorswithReplacement");
exit(1);
}
}
//check that groups are valid
for (int i = 0; i < userGroups.size(); i++) {
if (isValidGroup(userGroups[i], allGroups) != true) {
- mothurOut(userGroups[i] + " is not a valid group, and will be disregarded."); mothurOutEndLine();
+ m->mothurOut(userGroups[i] + " is not a valid group, and will be disregarded."); m->mothurOutEndLine();
// erase the invalid group from userGroups
userGroups.erase(userGroups.begin()+i);
i--;
//if the user only entered invalid groups
if (userGroups.size() == 0) {
- mothurOut("You provided no valid groups. I will run the command using all the groups in your groupfile."); mothurOutEndLine();
+ m->mothurOut("You provided no valid groups. I will run the command using all the groups in your groupfile."); m->mothurOutEndLine();
for (int i = 0; i < allGroups.size(); i++) {
userGroups.push_back(allGroups[i]);
}
}
catch(exception& e) {
- errorOut(e, "SharedUtil", "setGroups");
+ m->errorOut(e, "SharedUtil", "setGroups");
exit(1);
}
}
//check that groups are valid
for (int i = 0; i < userGroups.size(); i++) {
if (isValidGroup(userGroups[i], allGroups) != true) {
- mothurOut(userGroups[i] + " is not a valid group, and will be disregarded."); mothurOutEndLine();
+ m->mothurOut(userGroups[i] + " is not a valid group, and will be disregarded."); m->mothurOutEndLine();
// erase the invalid group from userGroups
userGroups.erase(userGroups.begin()+i);
i--;
if ((mode == "collect") || (mode == "rarefact") || (mode == "summary") || (mode == "treegroup")) {
//if the user only entered invalid groups
if ((userGroups.size() == 0) || (userGroups.size() == 1)) {
- mothurOut("When using the groups parameter you must have at least 2 valid groups. I will run the command using all the groups in your groupfile."); mothurOutEndLine();
+ m->mothurOut("When using the groups parameter you must have at least 2 valid groups. I will run the command using all the groups in your groupfile."); m->mothurOutEndLine();
for (int i = 0; i < allGroups.size(); i++) {
userGroups.push_back(allGroups[i]);
}
}
catch(exception& e) {
- errorOut(e, "SharedUtil", "setGroups");
+ m->errorOut(e, "SharedUtil", "setGroups");
exit(1);
}
}
//check that groups are valid
for (int i = 0; i < userGroups.size(); i++) {
if (isValidGroup(userGroups[i], allGroups) != true) {
- mothurOut(userGroups[i] + " is not a valid group, and will be disregarded."); mothurOutEndLine();
+ m->mothurOut(userGroups[i] + " is not a valid group, and will be disregarded."); m->mothurOutEndLine();
// erase the invalid group from globaldata->Groups
userGroups.erase(userGroups.begin()+i);
i--;
userGroups.push_back(allGroups[i]);
}
}
- mothurOut("When using the groups parameter you must have at least 2 valid groups. I will run the command using all the groups in your groupfile."); mothurOutEndLine();
+ m->mothurOut("When using the groups parameter you must have at least 2 valid groups. I will run the command using all the groups in your groupfile."); m->mothurOutEndLine();
}else if (userGroups.size() == 1) {
- mothurOut("When using the groups parameter you must have at least 2 valid groups. I will run the command using all the groups in your groupfile."); mothurOutEndLine();
+ m->mothurOut("When using the groups parameter you must have at least 2 valid groups. I will run the command using all the groups in your groupfile."); m->mothurOutEndLine();
userGroups.clear();
for (int i=0; i < allGroups.size(); i++) {
if (allGroups[i] != "xxx") {
}else if ((mode == "unweighted") || (mode == "parsimony")) {
//if the user only entered invalid groups
if ((userGroups.size() == 0) && (numGroups == 0)) {
- mothurOut("When using the groups parameter you must have at least 1 valid group. I will run the command using all the groups in your groupfile."); mothurOutEndLine();
+ m->mothurOut("When using the groups parameter you must have at least 1 valid group. I will run the command using all the groups in your groupfile."); m->mothurOutEndLine();
for (int i = 0; i < allGroups.size(); i++) {
if (allGroups[i] != "xxx") {
userGroups.push_back(allGroups[i]);
}
}
catch(exception& e) {
- errorOut(e, "SharedUtil", "setGroups");
+ m->errorOut(e, "SharedUtil", "setGroups");
exit(1);
}
}
}
}
catch(exception& e) {
- errorOut(e, "SharedUtil", "getCombos");
+ m->errorOut(e, "SharedUtil", "getCombos");
exit(1);
}
}
return false;
}
catch(exception& e) {
- errorOut(e, "SharedUtil", "isValidGroup");
+ m->errorOut(e, "SharedUtil", "isValidGroup");
exit(1);
}
}
}
}
catch(exception& e) {
- errorOut(e, "SharedUtil", "updateGroupIndex");
+ m->errorOut(e, "SharedUtil", "updateGroupIndex");
exit(1);
}
}